Jim,
You are ‘slightly’ ahead of the curve here, there are a number of things that Adobe needs to iron out before we’ll know how, what and where we should be encoding H.264 for Flash. For example the file extension will be .f4v, not .flv. An that was only announced in the last couple of weeks.
Suffice to say, Squeeze will need an update before it’s going to be ready to do the job for you.
It maybe a good idea in the interim to experiment with H.264 encodes just so you are more familiar.